Fig. 6

Distribution and genetic structure of a four-allele clique in Salmonella genomes. a A ring plot displaying co-occurrence events (red track) of the four alleles (darker boxes in grey tracks) against a midpoint-rooted phylogenetic tree of the Salmonella genomes. Clades are coloured by their top-10 most correlated PCs that significantly explained the presence-absence status of an arbitrarily designated response allele sul2. Tips highlighted with red circles denote genomes where the exact 3,084 bp MDR region harbouring all the four alleles were found using nucleotide BLAST. b A putative 6,790 bp plasmid sequence restored from the assembly graph of genome ERR026101. Alleles of four AMR genes were identified in this plasmid, showing 100% nucleotide identity and coverage to reference sequences of these genes